Pokemon Mystery Dungeon: Bonds Through Time
by Kagaminelover657
Summary: As the Keyblade War grows nearer, Sora and Kairi are sent by Yen Sid to the Pokémon World to stop the Organisation's plan. But when things go wrong, Roxas and Namine wake up on a random beach with little memory of what happened beforehand. With help from a Pikachu, they must track down Organisation XIII in Sora and Kairi's stead. But why are they here instead of Sora and Kairi?


**This is my first time involving Pokémon in my fanfiction, so I apologise if it isn't very good. To be honest, I don't know how I got this idea. But I'm surprised at how well it works with Pokémon Mystery Dungeon. I honestly hope you enjoy the first chapter.**

**Disclaimer: I don't own Pokémon or Kingdom Hearts.**

* * *

Chapter 1: A New Adventure Awaits

"Riku, wait up! You know Kairi and I can't keep up with you!"

Riku chuckled smugly to himself as he raced across the sand of the play islands away from the boats. Sora quickly leapt onto the sand and dashed as fast as he could after Riku, with Kairi close behind him. Kairi laughed playfully as the two chased after him, kicking small grains of sand up behind them.

It had been a while since the three of them had finally been reunited on Destiny Islands together. Of course, this would be the only time they could allow this to happen. Yen Sid had warned the trio that the Keyblade war was close to occurring. Kairi needed immediate training in order for her to be able to wield the Keyblade. Sora had been put in charge of training Kairi, while Riku was to train Lea. Tomorrow Yen Sid was planning on giving Kairi and Sora a chance to help out another world in order to contribute to Kairi's Keyblade training. The three friends wouldn't see each other for quite some time. So while they were still together, they were going to make the most of it.

Riku dashed along the peer towards the mini island, finally reaching the tree bough that was bent over where the three would always sit. The sun was beginning to set along the horizon as Sora and Kairi finally caught up with Riku. Sora put his hand against one of the palm trees to steady himself, panting.

"Geez Riku! You could have at least slowed down so we could catch up!"

Riku smirked, leaning his back against the tree trunk with his arms folded.

"And allow you two to miss the sunset? I don't think so"

Sora quickly dashed forward and pulled himself up onto the tree trunk, dangling his legs over it and sitting on the left side. Kairi copied him, placing herself beside him. Riku remained where he was, staring out intently towards the sunset. Kairi smiled a little, placing her hands in her lap.

"And to think that two years ago we were sat here wondering whether there were any other worlds out there…"

Riku chuckled a little.

"I know. I never would have thought we would be out saving the worlds from Xehanort at this point at all. It's something I would never have imagined happening"

Sora sat back on the tree trunk, with his trademark grin spread wide across his face.

"Well I'm pretty sure you can believe it now Riku. But I can't believe so much has happened in two years of us being separated"

Kairi sighed.

"And now we have a war to prepare for that will determine the fate of the worlds…"

Sora glanced at his two friends with a smile on his face.

"It's all for the better Kairi. It may not have been our war to start with, but I'm willing to do anything I can to protect the people and home that I care about. It's better than doing nothing at all"

"I agree Sora" Riku added. "I'm willing to do the same. Let's all do well in our training tomorrow, and give it our all"

Kairi nodded quietly in response. She closed her eyes, feeling a small breeze brush past and blow her hair back a little. She imagined the three of them sat back on the island again two years ago, two days before they were going to board the raft…

* * *

"_So, suppose you get to another world. What would you do there?"_

"_Well, I haven't really thought about it. It's just… I've always wondered why we're here on this island. If there are any other worlds out there, why did we end up on this one? And suppose there are other worlds… Then ours is just a little piece of something much greater. So we could have just as easily ended up somewhere else, right?"_

"_I don't know"_

"_Exactly. That's why we need to go out there and find out. Just sitting here won't change a thing. It's the same old stuff. So, let's go"_

* * *

Kairi almost chuckled at the memory. It would always be a childish dream within her memories, the one which will always be remembered as the start of their separate journeys.

The three of them sat in silence for a small while, savouring the moment as best as they could. The sky had now turned a dark shade of purple. The sun's rays gave the waves rolling towards the beach of the island a lovely glistening effect. The scenery was a very beautiful thing to behold. It was a view that these three teenagers would always remember, and would always share with each other whenever they got the chance to.

Sora lay back on the trunk sideways so he didn't fall off, putting his arms behind his head. A sudden thought struck his mind.

"Say, are we ever going to use that raft we built?"

It took a moment for Kairi and Riku to allow it to sink in, before the two of them burst out into loud and hearty laughter. Sora soon joined them. The only noise that could be heard on the whole island was the three friends' joyous laughter. When the three had finally calmed down, Riku shrugged.

"Sora, I highly doubt there is any point of us using that raft now. We could use it in emergencies though. Speaking of the raft, is it still where we left it?"

"I have no idea. I haven't been down to the cove in a while" Kairi replied. "Should we go and check before we leave?"

Riku smirked, standing up straight again and unfolding his arms.

"Yeah, we should. I'll race you both!"

Riku started dashing off across the peer again, chuckling to himself. Sora raised an eyebrow playfully.

"Riku! Wait up!"

He and Kairi quickly leapt down off the tree trunk and dashed after him as the sun finally set over the horizon. The island slowly turned back to its peaceful state. The only sounds that could be heard were the three friends' laughter.

* * *

The room was very quiet inside Yen Sid's tower. Starting from the left, Sora, Kairi, Riku and Lea were stood in a straight line in front of Yen Sid's desk, waiting silently for him to speak. King Mickey, Donald and Goofy stood behind Yen Sid's desk to the right, also waiting for the elderly wizard to speak. Everyone was being silent for a very good reason. They knew the topic at hand was a very serious and dangerous one. That's usually the only reason why everyone was called forth to the tower in the first place. Of course, the four Keyblade wielders knew well of why they had been called here, since they had been waiting for this day to arrive for quite some time.

Yen Sid sat forward in his chair and gently stroked his long and grey beard with one hand as he contemplated on his words. He eyed the four Keyblade wielders in front of him very intently. They could tell from his actions this was becoming very dire now.

"After all these years of battling the darkness, the final end to this long endured war is finally starting to come to a close. We finally know of Xehanort's plans, and now we must put an end to it once and for all. The Keyblade War is drawing ever closer, and so far Xehanort has been one step ahead of us every time. This time however, we are going to ensure that we prepare ourselves quickly and efficiently for the grave challenges ahead"

Yen Sid looked carefully between Lea and Kairi.

"Now that we have two new Keyblade wielders in our ranks, we must make sure they are fully prepared for the dangers that Xehanort may bring about. Therefore, you both must train under Sora and Riku so you may face the real Organisation XIII in the Keyblade War. After some discussion between the King and I, we have assigned the two of you individual missions to undertake in order to aid your training"

Yen Sid slowly turned to face Lea and Riku.

"Lea and Riku, you two have been given the task to venture into the Dark Realm to find a woman named Aqua. She is one of the seven pure lights that we need to fight in this Keyblade War. Once you find her, ask her to lead you to the other one of the seven pure lights, Ventus, in Castle Oblivion. She knows where Ventus is hidden I believe, since when I last saw her, she wanted to make sure her friend was protected, and so took Ventus with her. But please be warned that there are strong forces within the Realm of Darkness. You must be cautious and aware at all times. Understand?"

Riku and Lea nodded stiffly in reply. Yen Sid glanced towards Kairi and Sora, pleased with Riku and Lea's response.

"Very good. And Kairi and Sora, you have a mission which needs investigating urgently. The Real Organisation XIII members have been spotted wandering around a world inhabited mainly by creatures known as "Pokémon". This world is full of darkness, meaning it is a perfect haven for the Organisation to thrive. Something there seems to have piqued their interest. You need to investigate what they are after and put a stop to it. I fear they may be trying to sabotage our chances of protecting Kingdom Hearts. Do you both understand?"

Kairi and Sora nodded stiffly. Yen Sid nodded in approval.

"Very good. The Gummi Ship is prepared to take the four of you to your destinations. Prepare for your journeys and then let us know when you are ready to depart. I wish the four of you good luck"

* * *

Lea yawned as he sat back in his chair on the Gummi Ship.

"It's been two hours and no one has left the Gummi Ship yet. Are we even going at full speed?"

Riku rolled his eyes playfully as he sat on the window ledge of the ship, staring out at the many worlds they were currently passing by with his arms folded. Kairi and Sora were also sitting in their chairs. Sora chuckled a little at Lea's comment.

"Not everything can be done just like that Lea!"

"I know, but surely they could have picked places where we would be able to answer the urgency of the situation quicker"

"Sadly Lea, Yen Sid never chose those locations. Fate did" Riku replied, still staring out the window.

"True. Very true"

Kairi was silent as she too stared longingly out the window along with Riku.

"The worlds seem to be at peace, at least for now…"

"And hopefully that's how they shall stay" Riku added, sighing. "If only we knew what would happen once Kingdom Hearts was unlocked…"

"Sadly, we will never know" Lea replied. "And it's probably best we don't. I mean, if we did know, it would have probably caused more than what the first Keyblade War did. All we know is that it will affect all the worlds. We don't know in what way however"

"I heard the worlds could be recreated if Kingdom Hearts was opened" Sora commented quietly. "So that explains why Xehanort is so willing to start another Keyblade war"

"And if he were to get access to Kingdom Hearts…" Kairi began, trailing off.

She didn't even need to say it. All four of them knew the fate of the worlds if Xehanort managed it…

A sudden jolt startled the four Keyblade wielders as they glanced out the windows nearest each of them to find the Gummi ship had come to a sharp stop.

"We've reached the world of Pokémon!" Chip and Dale both screeched from somewhere above them.

Lea grinned towards Sora and Kairi.

"Looks like this is your stop"

Sora and Kairi glanced at each other for a short moment, before they both gave a stiff nod and slowly stood up. Riku turned his head slightly so he could see them both clearly.

"Take care of yourselves. Don't make me and Lea have to come in and save you"

Kairi raised an eyebrow towards Riku playfully.

"Someone's being Mr Cocky, aren't they?"

Riku chuckled a little.

"But seriously, be careful"

"What Mr Cocky said" Lea added, sniggering.

Riku rolled his eyes at him.

"Very funny Lea…"

Sora flashed Riku his trademark grin.

"Good luck to you both. We'll be back before you know it"

"Same to you"

Kairi and Sora slowly walked towards the other end of the Gummi Ship, preparing to exit it. They gave Lea and Riku one quick wave as they left. Riku sighed heavily as he turned to face the window once again, staring out towards the worlds currently in his view. Lea slumped in his chair and silently stared up at the ceiling for a moment.

"You know, instead of Mr Cocky, you should have been called Mr Worrywart"

Riku quickly turned to face him confused.

"Huh?"

"You doubt your friends' capabilities too much Riku. You got to learn to relax and put some faith in them. I know it's Kairi's first time using the Keyblade, and I know we almost lost Sora to the darkness, but they'll be fine. Trust me"

Lea grinned innocently at him. Riku was still unsure. He needed confirmation.

"How do you know?"

Lea shrugged, turning his gaze back to the ceiling.

"I don't know. I'm just listening to my gut"

Riku silently turned back to the window as the Gummi Ship prepared to move again.

(Sora… Kairi… Please stay safe…)

* * *

Sora slowly walked forward, glancing in shock at his surroundings. Yen-Sid wasn't kidding when he said the place was completely consumed by darkness. He had been right. The ground, the sky, everything was coloured a light grey. It was silent. There was no colour to be seen at all. It was very off putting and depressing.

Sora continued to scan the area around him silently as Kairi slowly came up beside him. She was just as shocked as he was. Sora's eyes fell upon a nearby tree just in front of them. They were near a forest by the looks of things. But this particular tree had a drop of water hanging off the end of a leaf that appeared to be frozen. Sora frowned at this. It was as if all of time had frozen, and all of life had been sucked away. Kairi shuddered, feeling a nasty chill run up her spin.

"What has happened to this world? It looks so barren… Is there anyone even here?"

Sora shrugged a little.

"I don't know Kairi. But one thing I can confirm is that this world has given in to the darkness…"

Kairi realised there was no breeze, or any indication of wind blowing whatsoever. And the two had also realised that there were no Heartless around here either. It was silent, and barren. Just what was going on here?

"Why would the real Organisation want to come here for?"

"Your guess is as good as mine Kai. Something isn't right. I don't like the silence…"

Sora and Kairi both froze then as a loud cry of agony resounded from somewhere within the forest. Someone was here after all, and they were in trouble. Reacting out of instinct, Sora quickly summoned his Keyblade and charged towards the source of the noise.

"Sora!"

Kairi summoned her Keyblade and quickly dashed after him, not wanting to be left behind. As they gained closer and closer, small chuckling could be heard. And it wasn't nice chuckling either. It was more like an evil type of chuckle. And funnily enough, all the chuckling sounded the same. Sora found this odd, but dashed towards the clearing anyway with Kairi close behind.

In the middle of the clearing was a weird looking green Gecko trying to fight off five purple creatures that resembled the Heartless a little. They were stood on two feet only, as was the Gecko. Their eyes looked like crystals, and they had a red ruby like stone on their chest. Their ears were pointed in an odd shape. Sora didn't like the look of them. Were they a new kind of Heartless? He and Kairi were about to find out!

The Gecko was down on one knee when Sora leapt in out of nowhere and slashed viciously at the purple creature about to attack it with his Keyblade. The purple thing reared back immediately, crying out in shock and surprise.

"H-Humans with weapons?! Retreat! Retreat! We must alert of this to Dusknoir!"

The other four screeched out in fright and quickly scattered in random directions, leaving Kairi and Sora standing there confused. They had no idea what had just happened. These creatures could talk too? And they didn't vanish like the Heartless did either. They just ran away.

(Are these the "Pokémon" that Yen-Sid mentioned…?) Sora wondered to himself.

Kairi was startled by the sudden groan of agony behind her. She glanced back to find the Gecko trying to get to its feet. Summoning away her Keyblade, she carefully approached it.

"Are you alright?"

The Gecko looked between the two of them silently for a moment before responding.

"I have never seen humans wielding a weapon before. I guess I owe you both… T-Thanks…"

The Gecko sounded male. He stumbled a little, lingering on his left foot in an attempt to keep his balance. Kairi steadied him by holding onto his shoulders gently, kneeling down beside him. Sora knelt down on his other side, frowning a little.

"What were those things that attacked you?"

"S-Sableye. They are deadly Pokémon that work for Dusknoir"

"Dusknoir…? Is he a Pokémon too?"

The Gecko frowned at Sora confused.

"How can you not know that?"

He rubbed the back of his head sheepishly.

"We're not really from around here…"

The Gecko looked between both him and Kairi again.

"Ah… That explains why you wield those strange weapons…"

The three froze at the sound of the Sableye chuckling.

"We need to move. They've sent for Dusknoir, and he's probably sent more of them to come after me and possibly you two"

"But you can't walk properly" Kairi protested, glancing up at Sora. "What should we do?"

Sora looked down at the Gecko curiously.

"Well, I could carry him on my shoulders. As long as he guides the way, we should be fine"

The Gecko nodded in agreement.

"Thank you. I know where we can hide from them. But we'll have to hurry"

Sora carefully picked the Gecko Pokémon up under his arms and sat him upon his shoulders, slowly standing up. Kairi stood up as well at the sound of a group of footsteps thudding their way towards them loudly. The Gecko wrapped his arms tightly around Sora's forehead as they ran away from the area as quickly as they could.

"It's just up ahead!"

Sora nodded as the trio approached a large cliff on the edge of the forest. There was a crevice in the side of it big enough for the three of them to hide in. Sora was the first one to enter. He quickly ducked down, stepping into the darkness while half crouching. Kairi carefully followed closely behind as Sora gently placed the Gecko on the floor sitting down in a corner. He and Kairi then sat opposite him on the other side of the little cave like crevice silently. Kairi glanced out towards the forest.

"Have the Sableye given up?"

"They should have by now" The Gecko replied, keeping his voice low. "The Sableye don't tend to chase after criminals for very long"

"Criminals? You're a criminal?" Sora repeated, confused.

"In their eyes I am…"

The Gecko paused then, realisation suddenly hitting him.

"How rude of me. I forgot to introduce myself. The name's Grovyle, currently this world's most dangerous outlaw"

The Pokémon, now revealed to be Grovyle, rolled his eyes at his own remark. Sora smiled a little, trying to lighten up the situation and mainly to be polite.

"I'm Sora. And this is my friend Kairi"

Kairi nodded in acknowledgement, smiling slightly.

"It's nice to meet you Kairi and Sora. Although, I wish it had been under better circumstances…"

"Why are you seen as an outlaw?" Kairi questioned.

Grovyle shifted his position slightly so that his back was straighter against the wall, trying to get comfortable.

"It's a long story…"

"We've got time" Sora replied, leaning back a little. "Does it have something to do with the current state of this place?"

Grovyle nodded.

"Sadly yes… It all started many years ago. This world was once lively and happy. Humans and Pokémon alike got along perfectly fine. Everything was peaceful. And then an unknown phenomenon started to take its toll; The Planet's Paralysis began. It started with the Time Gears"

"Time Gears?"

"Yes. The Time Gears were once sacred relics that were scattered throughout this world in hidden areas. They kept time flowing in certain regions. Yet for some reason, time in those areas suddenly began to stop. No one knew how or why this was happening, but it soon began to spread like a fire to each area. And then one day, Temporal Tower collapsed and sealed this world's fate"

"Temporal Tower?" Kairi repeated.

Grovyle nodded, pointing out of the crevice towards a large and tall tower in the distance. Sora and Kairi followed his finger curiously.

"That is Temporal Tower. The Legendary Pokémon Dialga, the controller of time itself, is situated there. On the day Temporal Tower collapsed, Dialga lost control of himself. He is now known as Primal Dialga, the Legendary Pokémon of Darkness. He is responsible for our corrupted world. All Pokémon here have now turned to the darkness, well except me"

"That sounds awful. And no one could stop it?"

"No one could stop it. No one expected it to happen. And now Primal Dialga has made it his goal to find and arrest anyone who dares try to change the course of history, using Dusknoir and his army of Sableye"

"Is that why you're classed as an outlaw?" Sora asked.

Grovyle nodded silently. Sora shook his head in disbelief.

"That's not right…"

"Sadly Sora, the darkness is never fair" Grovyle continued, sighing heavily. "And now you two have been brought into it. Bounties will go over your heads too"

"What will happen if they catch us?"

Grovyle downcast his gaze towards the floor.

"The penalty for such a crime will be death, most likely…"

Sora's and Kairi's eyes widened in horror.

"Death?" Kairi repeated, stunned. "Isn't that harsh?"

"In a way it isn't. Because what Grovyle is trying to do is a world changing thing. If they class fixing this world as a crime then the punishment will come out just as bad, right?"

"Precisely Sora. That is how Primal Dialga thinks"

"But what could you possibly think to do that is a threat to this world?" Kairi pressed.

Grovyle leaned forward a little, lowering his voice slightly.

"There's a way to change time and history for the better: Time Travel"

Sora frowned. That was possible? But that was when he remembered what Riku had told him about Xehanort's time travel.

"You can time travel?"

Grovyle nodded.

"Yes. There is a way to travel back through time and into the past. I plan to go back there and change the future"

Sora frowned at this.

"I thought you weren't allowed to alter the events of the future"

"You aren't supposed to, but it is possible"

Sora was getting confused with what Xehanort had already told Riku and Mickey, but he stayed silent. It was clear that Grovyle could be trusted. He knew what he was talking about.

"And how do you plan to change the future in the past?"

"Using the Time Gears"

Grovyle turned back towards Temporal Tower.

"Inside Temporal Tower, right at its peak, there is a small alter. That alter has five indents where the Time Gears can be slotted. By taking the Time Gears to Temporal Tower and slotting them into the alter, I can prevent the Planet's Paralysis. Although it will temporarily stop time within the five areas the Time Gears come from. Pokémon from the past will soon notice the changes, and seek to hunt down the thief. It is a risk I am willing to take however. I want the future to be better and brighter for all Pokémon, even if it means making sacrifices"

Sora was stunned at the resolve this Pokémon had. Even Kairi was quite shocked at his words. Grovyle soon sighed.

"If only I could do that… Sadly I'm not making much progress currently. Now that Primal Dialga has those black cloaked humans on his side, the Sableye have found it a lot easier to track my movements"

"Black cloaked humans? Sora, could they be…?" Kairi questioned, trailing off.

"Organisation XIII? Most likely"

"You know those cloaked humans?"

Sora nodded stiffly.

"Of course we do. That's the exact reason why we're here. We've been sent to stop the Organisation"

Grovyle leaned back against the wall thoughtfully.

"It seems our missions correspond"

Kairi sighed heavily, bringing her knees up to her chest and hugging them tightly.

"It seems our mission has just gotten a lot harder. With the Organisation working alongside this Legendary Pokémon, and also with the Sableye hunting all of us down, we may never save this world from the darkness…"

"I wouldn't say that Kairi"

Sora stood up, scratching the back of his head thoughtfully. Kairi frowned at him confused.

"What do you mean, Sora?"

He glanced between both Grovyle and Kairi, his arms now folded.

"Well, Grovyle is trying to change the course of history for the better. We are trying to put a stop to the Organisation's plans. Both our goals reach the same conclusion: This world is saved. So, since the Organisation have teamed up with Grovyle's enemies, how about the three of us work together and find the Time Gears?"

Grovyle's eyes widened in surprise.

"You'd risk helping me? A _criminal_?"

Sora flashed Grovyle his famous trademark grin.

"Kairi and I are criminals now too, aren't we? We might as well stick together and help each other out! Also, I'm not one to turn away from someone who needs help!"

Kairi nodded in agreement, with determination in her eyes.

"I agree with Sora. If we all work as a team, we can take down our enemies together. There's always strength in numbers"

For the first time in a while, Grovyle found himself smiling a genuine smile. He could sense that both Kairi and Sora held a strong resolve also, and like many others who had encountered them before, he began to feel drawn to their light.

"You both have my thanks. I hope that one day I can return the favour for your kindness. With your help, the future will at last be restored to its former glory. That I am sure of"

Kairi glanced back outside towards the quiet and still forest.

"Should we start moving again before the Sableye find us?"

"That might be wise" Grovyle replied as he tried to stand up.

Sora steadied him before carefully placing him back on his shoulders again.

"You can tell us what we should do next along the way. That should save us time then"

Grovyle nodded silently in agreement as the three of them exited the crevice, and began making their way carefully through the forest once again.

* * *

"What do you mean you lost them?!"

Loud yelps came from the small group of Sableye as they dodged another attempt to lash out at them from Dusknoir. The one nearest to Dusknoir swallowed hard, preparing to speak.

"B-B-But Lord Dusknoir, they were too fast for us!"

"I don't want to hear your excuses! I want them found and brought back to Temporal Tower immediately! Understand?"

"Yes Lord Dusknoir!" They all cried in sync before scattering off in different directions.

Dusknoir watched his underlings scatter before letting out a huge sigh. He turned slightly towards a figure in a black cloak beside him. They had their hood up, concealing most of their face.

"So you say you know who those humans with weapons are?"

The hooded figure nodded stiffly.

"That I do. From what your underlings have described, they make me picture two specific individuals who wield the mighty weapon that is the Keyblade. And if my assumption is correct, then they did not appear here by mere accident"

"They are dangerous?"

"Inevitably. If they team up with that Pokémon, they will most likely succeed"

"So they must receive the penalty along with Grovyle?"

"That they must. You know the consequences their success will bring about if you allow that to happen, don't you?"

Dusknoir frowned.

"Of course I'm aware, as is Master Dialga!"

"Then you must ensure you do not fail"

Dusknoir glanced back towards the forest.

"I will definitely ensure that, for the safety of our future…"

* * *

**Please let me know whether I should continue writing it or not. Your feedback is greatly appreciated. Thank you for reading.**


End file.
